recipe bioconductor-hicbricks

A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/HiCBricks.html

License

MIT + file LICENSE

Recipe

/bioconductor-hicbricks/meta.yaml

package bioconductor-hicbricks

Versions

1.0.0-0

Depends

• bioconductor-biocfilecache >=1.6.0,<1.7.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-rhdf5 >=2.26.0,<2.27.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• r-base >=3.5.1,<3.5.2.0a0

• r-curl

• r-data.table

• r-digest

• r-ggplot2

• r-r6

• r-rappdirs

• r-rcolorbrewer

• r-reshape2

• r-scales

• r-stringr

• r-viridis

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-hicbricks

and update with:

conda update bioconductor-hicbricks

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-hicbricks:<tag>

(see bioconductor-hicbricks/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-hicbricks/README.html)